The DOI matches its Crossref record; 127 of the 127 references it cites were found in a registry or an index; 16 of the 68 sources its claims cite were checked for support.
Rethinking phylogenetic comparative methods
Open accessPublished version of a preprint
Abstract
As a result of the process of descent with modification, closely related species tend to be similar to one another in a myriad different ways. In statistical terms, this means that traits measured on one species will not be independent of traits measured on others. Since their introduction in the 1980s, phylogenetic comparative methods (PCMs) have been framed as a solution to this problem. In this article, we argue that this way of thinking about PCMs is deeply misleading. Not only has this sowed widespread confusion in the literature about what PCMs are doing but has led us to develop methods that are susceptible to the very thing we sought to build defenses against-unreplicated evolutionary events. Through three Case Studies, we demonstrate that the susceptibility to singular events is indeed a recurring problem in comparative biology that links several seemingly unrelated controversies. In each Case Study, we propose a potential solution to the problem. While the details of our proposed solutions differ, they share a common theme: unifying hypothesis testing with data-driven approaches (which we term "phylogenetic natural history") to disentangle the impact of singular evolutionary events from that of the factors we are investigating. More broadly, we argue that our field has, at times, been sloppy when weighing evidence in support of causal hypotheses. We suggest that one way to refine our inferences is to re-imagine phylogenies as probabilistic graphical models; adopting this way of thinking will help clarify precisely what we are testing and what evidence supports our claims.
Overview
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Written from the paper’s full text.
TL;DR
The paper argues that phylogenetic comparative methods are commonly mischaracterized as solving nonindependence and are instead vulnerable to singular, unreplicated evolutionary events that can generate spurious associations. Through three case studies it recommends combining hypothesis testing with data-driven “phylogenetic natural history” and using graphical models to clarify causal inference.
Key findings
- Across continuous and discrete comparative methods, a single unreplicated shift can drive significant associations; in Felsenstein’s worst-case simulations, as shift variance relative to BM variance increases, the proportion of significant contrast regressions increases dramatically (each point represents 200 simulations for a fixed phylogeny).
- Reanalysis of the Scales et al. (2009) data set of fast glycolytic muscle fiber fraction across 22 squamate lizards found the original predator-escape (PE) hypothesis was 13.0 AICc units better than the next closest model (FMPE), but a Bayesian mixture with RJMCMC gave intermediate weight to PE on empirical data and recovered only a single highly supported shift on the stem branch of *Phrynosoma*; combined analysis gave strongest support to a *Phrynosoma*-only model, intermediate support to PE, and little support to the reversible-jump component.
- For discrete traits under Darwin’s scenario, Pagel’s correlation test statistic reduces to \(D = 2(\ln(T)-\ln(t))\), so support for the dependent model increases with total tree length; simulations on 20-taxon trees matched this prediction.
- The authors recommend unifying hypothesis testing with data-driven “phylogenetic natural history” and rendering phylogenies as probabilistic graphical models/Bayesian networks to clarify causal assumptions.
Methods
- Conceptual synthesis with three case studies; no single empirical data set spans all analyses.
- Case I simulations used a two-clade phylogeny (unresolved or Yule fully bifurcating), two traits under independent Brownian motion with \(\sigma^2 = 1\), and a singular event on a stem branch drawn from a multivariate normal with uncorrelated equal variances that were a scalar multiple of \(\sigma^2\); Case III derived Pagel’s test under Darwin’s scenario and simulated 20-taxon trees in diversitree with irreversible transitions on one randomly chosen internal branch, constrained vs. unconstrained Pagel models, root state 0, and loss rates 0.
- Case II built a Bayesian mixture model on the R package bayou, reanalyzing the Scales et al. (2009) 22-squamate data set and simulated data sets; expected trait values were a weighted average of a fixed PE regime painting and an RJMCMC-estimated shift configuration, with a truncated Poisson prior on number of shifts (mean 0.5, maximum 10) and a symmetric beta(0.8, 0.8) prior on the weight parameter.
Limitations
- Stated by the authors: the “singular events” model is primarily illustrative; fitting realistic cases requires estimating the location and number of events; there is no one-size-fits-all solution; many details remain to be worked out and alternative paths were not considered.
- Stated by the authors: in Case II, vague priors on the number and location of shifts in the reversible-jump analysis reward correctly guessing which branch contains a shift; ascertainment bias is likely prevalent; Darwin’s scenario is a boundary case, and the derivation’s assumptions differ slightly from available software.
- Evident from the text: Case II is limited to one 22-species lizard data set plus simulated data sets, and Case III’s analytical result assumes traits were selected without first looking at their phylogenetic distribution—a condition the authors say is rarely met.
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Claims the paper makes
71 Own interpretation · 24 No full text of the sources · 18 No basis given · 16 Own result · 5 Supported so far · 5 Partly supported · 3 Supported · 2 Sources not found · 2 Not checked yet · accuracy not yet measured
The sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“The work of Beaulieu and O'Meara (Beaulieu et al. 2013;Beaulieu andO'Meara 2014, 2016) has illuminated important underlying reasons behind Rabosky and Goldberg's findings: the failure to consider alternative models in which the”
§ Rethinking phylogenetic comparative methods > Abstract
What the sources say
- Not checked — no full text of the sourcecites Beaulieu et al. 2013 source
- Supportedcites Beaulieu and O'Meara 2016 source
In “Multimodel Inference and the Issue of Appropriate Models,” the paper explains that a complex diversification history can make a trait-dependent model fit even when the trait evolves independently of diversification. In “BiSSE HiSSE,” it says that including alternative trait-independent diversification models should alleviate spurious assignments of rate differences to observed traits. Page numbers are not available in the supplied copy. (LLM, conf=0.91)
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In the paper
“We think that the solution proposed by Beaulieu and O'Meara (2016)-accounting for background shifts in evolutionary regimes unrelated to the focal trait association-is general and applies across comparative biology.”
§ Rethinking phylogenetic comparative methods > Abstract
What the sources say
- Supportedcites Beaulieu and O'Meara (2016) source
The paper describes expanding BiSSE to infer hidden states and including trait-independent diversification models alongside trait-dependent ones. In its BiSSE/HiSSE discussion, it says this should reduce spurious associations between diversification-rate differences and the focal trait. The claim that the approach applies across comparative biology is the citing authors’ own conclusion, not a result they attribute to this source. (LLM, conf=0.90)
plainn = 3- Asserted: passes — The authors put it forward as true.
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- Supported
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In the paper
“While this model is useful (and has often been used) for testing for adaptation, it is inconsistent with how we think of the process of adapting to an optimal state (Lande 1976;Hansen 1997;Hansen and Orzack 2005;Hansen et al. 2008;Hansen and Bartoszek 2012).”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
What the sources say
- Not checked — no full text of the sourcecites Lande 1976 source
- Supportedcites Hansen 1997 source
In “The Evolutionary Approach to a Primary Optimum” (page not available), Hansen describes adaptation as an approach toward an optimum. In “Results” (page not available), he says the model reduces to Brownian motion with a trend when the optimum is not reachable. This supports the cited contrast between Brownian motion and adaptation to an optimum. (LLM, conf=0.89)
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“a wide breadth of macroevolutionary data suggest that abrupt shifts and discontinuities have been a major feature of life on Earth”
§ Rethinking phylogenetic comparative methods > Abstract
What the sources say
- Partly supportedcites Uyeda et al. 2011 sourceExperimental — accuracy not yet measured
The paper’s opening section reports that a model combining rare, substantial bursts of phenotypic change with shorter-term bounded fluctuations best fits its data. But those data chiefly concern body size in mammals, squamates, and birds; they do not establish that abrupt shifts and discontinuities have been a major feature of life on Earth generally. (LLM, conf=0.85)
- Partly supportedcites Landis and Schraiber 2017 sourceExperimental — accuracy not yet measured
The Abstract describes evidence of rapid evolutionary pulses in fossil and ecological data, and the Discussion reports that jump models best explained body-size evolution in 32% of the 66 vertebrate clades studied. These passages support abrupt shifts as a feature of evolution, but the claim extends the finding to life on Earth generally; the paper says the prevalence of pulsed evolution across the Tree of Life remains unknown. Page numbers were not available in our copy. (LLM, conf=0.86)
- Supportedcites Jablonski 2017 source
In “Scale and Hierarchy” (page unavailable), the paper describes fossil-record stasis and mass extinctions that redirect evolutionary trajectories rather than following trends observed over shorter intervals. In “Contingency” (page unavailable), it calls rare events part of the fabric of macroevolution. Together, these passages support the broad claim that discontinuities are a major macroevolutionary feature. (LLM, conf=0.86)
hedged- Asserted: passes — The authors put it forward as true.
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- Partly supported
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In the paper
“Hansen's introduction of the Ornstein-Uhlenbeck (OU) process to comparative biology and the suite of methods built on his approach have been the only real attempts to actually try and capture the basic dynamics of adaptive trait evolution on phylogenies.”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
What the sources say
- Partly supportedcites Hansen 1997 sourceExperimental — accuracy not yet measured
In “The Evolutionary Approach to a Primary Optimum” (page unavailable), Hansen identifies his model as an Ornstein–Uhlenbeck process and describes a novel biological interpretation of it. But he explicitly says the process had previously been suggested for comparative studies, so the paper does not support saying he introduced it to comparative biology. The Abstract describes his method, but does not establish that methods built on it were the only attempts to capture adaptive trait evolution on phylogenies. (LLM, conf=0.88)
plain- Asserted: passes — The authors put it forward as true.
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- Partly supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“However, AIC provides only relative support for a model given a set of alternatives (see Pennell et al. 2015 for more on this point in the context of comparative methods).”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
What the sources say
- Supportedcites Pennell et al. 2015 source
The Discussion (“Why Does Model Adequacy Matter?”) says that comparing a model with alternatives using information-theoretic metrics permits only a relative assessment of its suitability. The Results specifically use AIC to identify the most highly supported model in a candidate set. (LLM, conf=0.94)
plain- Asserted: passes — The authors put it forward as true.
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- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Depending on the Bayesian network structure, the appropriate method of analysis can range from a nonphylogenetic regression (Fig. 7A), to commonly used comparative methods such as PGLS (Fig. 7B), to methods that require modeling both the evolutionary history of interaction of both trait X and trait Y (Fig. 7C) (Hansen 1997;Butler and King 2004;Hansen et al. 2008;Revell 2010;Hansen and Bartoszek 20”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
What the sources say
- Partly supportedcites Hansen 1997 sourceExperimental — accuracy not yet measured
The Phylogenetic Covariance section describes generalized least squares for phylogenetically correlated trait data, and the Discussion argues that comparative analyses should consider the history of selective regimes. The paper does not set out a Bayesian-network-based choice among nonphylogenetic regression, PGLS, and joint modeling of the evolutionary histories of two traits. Page numbers were not available in our copy. (LLM, conf=0.84)
- Not checked — no full text of the sourcecites Butler and King 2004 source
- Not checked — no full text of the sourcecites Hansen et al. 2008 source
plainconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“For PGLS and other linear modeling approaches, modeling the errors using fat-tailed distributions (Blomberg et al. 2012;Landis et al. 2012;Elliot and Mooers 2014;Duchen et al. 2017) may mitigate the impact of singular evolutionary events on the estimation of the slope (also see Slater and Pennell 2013, for an alternative approach using robust regression).”
§ Rethinking phylogenetic comparative methods > THE STRUCTURE OF A SOLUTION
What the sources say
- Not checked — no full text of the sourcecites Blomberg et al. 2012 source
- Partly supportedcites Landis et al. 2012 sourceExperimental — accuracy not yet measured
The paper’s introduction (page not available in our copy) says that Lévy-process jumps give trait-change distributions fat tails and account for abrupt evolutionary shifts. Its Discussion addresses detecting such jumps, but the paper does not show that fat-tailed errors mitigate their effect on slope estimates in PGLS or other linear models. (LLM, conf=0.82)
- Partly supportedcites Elliot and Mooers 2014 sourceExperimental — accuracy not yet measured
The Background toy example shows that a heavy-tailed stable model is less affected than a Brownian model by an unusually large change on one branch, but its outcome is ancestral-state reconstruction, not a regression slope. The Discussion proposes heavy-tailed methods for future studies of correlated evolution and notes that stable distributions lack the covariance matrix used in phylogenetic regression. It does not show that fat-tailed errors mitigate the effect of singular events on slope estimates in PGLS or other linear models; page numbers were not provided in our copy. (LLM, conf=0.85)
hedgedconditional- Asserted: passes — The authors put it forward as true.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The probability of the dependent model P(M dep |A) under Darwin's scenario is P(M dep |A) = (t/T) (7 )”
§ Rethinking phylogenetic comparative methods > CASE STUDY III: DARWIN'S SCENARIO AND UNREPLICATED BURSTS
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“When we simulated data under the PE hypothesis, the estimated weight given to the PE hypothesis was likewise high (Fig. 3B).”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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- Probably not a substantial claim. 27
- It may state two separate claims as one. 35
The sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“Tests of adaptive evolution come in two flavors: those with an a priori hypothesis (or hypotheses) regarding which lineages belong to which distinct regimes based on ancestral state reconstruction of explanatory factors (Butler and King 2004;Beaulieu et al. 2012) and those where the locations of regime changes are themselves estimated along with the parameters of the OU process (Ingram and Mahler”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
What the sources say
- Not checked — no full text of the sourcecites Butler and King 2004 source
- Supportedcites Ingram and Mahler 2013 source
The Forward Phase section says SURFACE places regime shifts using continuous trait data rather than a priori hypotheses. The Backward Phase section says its final model identifies where shifts occur and estimates the OU parameters, supporting the clause attributed to Ingram and Mahler. (LLM, conf=0.93)
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“For example, we highlighted in the introduction that we think HSMs (following Beaulieu et al. 2013;Beaulieu and O'Meara 2016) are a potentially powerful, and widely applicable solution, even though we did not consider these in detail here.”
§ Rethinking phylogenetic comparative methods > THE STRUCTURE OF A SOLUTION
What the sources say
- Not checked — no full text of the sourcecites Beaulieu et al. 2013 source
- Supportedcites Beaulieu and O'Meara 2016 source
The discussion passage beginning “Our HiSSE framework spans this range” (page unavailable in our copy) says the method can detect diversification driven by either a focal trait or an unexamined factor, including cases where both matter. That supports the citing authors’ hedged description of hidden-state models as a potentially powerful, widely applicable solution. (LLM, conf=0.88)
hedged- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
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In the paper
“These tools have been embraced by fields such as computer science, epidemiology and the social sciences, but largely ignored by comparative biologists [rare exceptions are the recent introductions of phylogenetic path analysis by Hardenberg and Gonzalez-Voyer (2013) and the application of causal models to make inferences from paleontological time-series by Reitan and Liow (2017)].”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
What the sources say
plain- Asserted: passes — The authors put it forward as true.
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Every source the paper cites for this claim was checked and supports it.
In the paper
“This fundamental problem has sown doubts about the suitability and reliability of many methods in comparative biology (e.g., Losos 2011), even if it was not obvious that these issues were connected.”
§ Rethinking phylogenetic comparative methods > THE STRUCTURE OF A SOLUTION
What the sources say
- Supportedcites Losos 2011 source
In “Many Traits in Many Clades Do Not Exhibit Phylogenetic Effect,” Losos says incorporating phylogenetic information may be unnecessary or inappropriate for some traits and questions how errors from comparative methods compare with errors from ignoring phylogeny. The Conclusions add that phylogenetic methods that ignore variation in evolutionary processes often produce inaccurate or misleading results. These passages support the cited doubt about the suitability and reliability of comparative methods. (LLM, conf=0.88)
plaindirectn = 3- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim.
- Supported
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In the paper
“Furthermore, we also think that rigorous examination of goodness-of-fit and model adequacy following any comparative analysis is critical for finding unforeseen singular events driving signal in the data set (Garland et al. 1992;Boettiger et al. 2012;Slater and Pennell 2013;Pennell et al. 2015).”
§ Rethinking phylogenetic comparative methods > THE STRUCTURE OF A SOLUTION
What the sources say
- Not checked — no full text of the sourcecites Garland et al. 1992 source
- Partly supportedcites Boettiger et al. 2012 sourceExperimental — accuracy not yet measured
The Introduction (§1.1; page unavailable) says comparative results can be difficult to interpret without assessing model fit, uncertainty, or power, supporting the value of rigorous evaluation. The cited paper does not say that post-analysis goodness-of-fit or model-adequacy checks reveal unforeseen singular events driving the signal in a dataset. (LLM, conf=0.82)
- Not checked — no full text of the sourcecites Slater and Pennell 2013 source
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. It may be too vague to check against evidence.
A claim is checked only against the cited paper’s full text, never its abstract, and none is available for its sources.
In the paper
“We also note that estimating a transformation for the errors (Pagel 1999;Freckleton et al. 2002) will not rescue the analysis; the estimated value of will lie between 0 and 1 and we have found both these more extreme cases (OLS and IC, respectively) to be susceptible.”
§ Rethinking phylogenetic comparative methods > CASE STUDY I: FELSENSTEIN'S WORST-CASE SCENARIO
What the sources say
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In the original Scales data set, there are weakly supported shifts in the clades leading to the sister group of Phrynosoma lizards, and the branch leading to Acanthodactylus scutellatus and Aspidoscelis tigris.”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Doing so recovers strongest support for the Phrynosoma-only model, intermediate support for the PE hypothesis, and very little weight on the reversible-jump hypothesis, which has no strongly supported shifts (Fig. 5).”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Here, we revisit Felsenstein's worst-case scenario in order to demonstrate that IC and Phylogenetic Generalized Least Squares (PGLS) do not completely address the problem that we tend to think they do-these methods are still susceptible to singular evolutionary events.”
§ Rethinking phylogenetic comparative methods > CASE STUDY I: FELSENSTEIN'S WORST-CASE SCENARIO
boosted- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In B and C, the correct model receives highest support with neither of the alternatives being well-supported.”
§ Rethinking phylogenetic comparative methods > CONCLUDING REMARKS: ARE OUR MODELS VALID
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The shading of the points indicates cases where this assumption is violated, as outlying points with max(Q) values much greater than 1/T (where only 1 shift is expected) are much more likely to fall off the predicted line.”
§ Rethinking phylogenetic comparative methods > CONCLUDING REMARKS: ARE OUR MODELS VALID
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- The authors state this as an assumption: The rates of gain of the traits are so low that only one shift is ever observed (in the Figure 6 analysis).
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In the original Scales data set, the Phrynosoma-only hypothesis receives the most weight (indicating a singular shift best explains the patterns observed in the data), while an intermediate weight is given to the PE hypothesis (which explains a good amount of the remaining variation).”
§ Rethinking phylogenetic comparative methods > CONCLUDING REMARKS: ARE OUR MODELS VALID
hedgeddirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Therefore, both networks can produce data sets with phylogenetic signal in both body size and migratory behavior, and both can produce a data set with the distribution in Figure 9D (see Supplementary Material available on Dryad for additional details on generating Fig. 9).”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We estimate a high posterior probability on a regime shift in the genus Phrynosoma from the empirical data only (red circle), indicating that while the PE hypothesis explains some patterns in the data, it does not fully explain the shift present in the behaviorally and ecologically unique genus Phrynosoma.”
§ Rethinking phylogenetic comparative methods > CONCLUDING REMARKS: ARE OUR MODELS VALID
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Rather, the great uncertainty in possible models is incorporated as a prior on the arrangement of shifts and is limited in explanatory power, something that researcher-driven biological hypotheses are much more capable of accomplishing.”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
plain- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“As discussed above, given a large enough tree such a priori hypotheses are likely to be strongly supported; if you can predict which one branch out of many will contain a shift then you may be on to something.”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“As with Case Study I, these scenarios ultimately reduce to whether or not coincident unreplicated events are evidence of a causal link between traits (Maddison and FitzJohn 2015), a problem we will address in Case Study III.”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
What the sources say
- Not checked — no full text of the sourcecites Maddison and FitzJohn 2015 source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Detecting a signal of evolutionary covariation is more difficult in discrete characters, but examining this situation isolates the recurring problem we have identified in the two previous Case Studies—whether or not coincident unreplicated events are evidence of causal links between traits.”
§ Rethinking phylogenetic comparative methods > CASE STUDY III: DARWIN'S SCENARIO AND UNREPLICATED BURSTS
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
In the paper
“Therefore, the conclusions of Scales et al. (2009) hold up, even when accommodating evolutionary regime shifts unrelated to the factors being considered, although the weight of evidence appears to be larger than it actually is.”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
What the sources say
- Not checked — no full text of the sourcecites Scales et al. (2009) source
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Furthermore, models that actually describe such scenarios-like our”
§ Rethinking phylogenetic comparative methods > CASE STUDY I: FELSENSTEIN'S WORST-CASE SCENARIO
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
In the paper
“Felsenstein also noted that the problem of nonindependence does not occur if”
§ Rethinking phylogenetic comparative methods > CASE STUDY I: FELSENSTEIN'S WORST-CASE SCENARIO
What the sources say
- Not checked — no full text of the sourcecites Felsenstein 1985 source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In fact, discovering the location of wellsupported shifts on the phylogeny does not say anything about causation; it is merely a descriptive technique to find major features of the data where there is evidence that the parameters governing the dynamics of trait evolution have shifted on the phylogeny.”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
plain- Asserted: passes — The authors put it forward as true.
- Checkable: unclear — It is unclear whether it could be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Multioptima OU models have been widely used to test for the presence of shifts in evolutionary regimes (i.e., parts of the phylogeny with their own optima, or less commonly, their own strength of selection parameters).”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
What the sources say
- Not checked — no full text of the sourcecites Butler and King 2004 source
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We show here that allowing for unaccounted shifts can provide a stronger test and more nuanced conclusions regarding the support for a particular predictor driving trait evolution across a phylogeny.”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The former (hypothesis testing) seeks to understand the causes of evolutionary shifts, while the latter (data driven) is a descriptive and exploratory approach to understanding evolutionary patterns.”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
plain- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Note that these scenarios do not differ qualitatively from Felsenstein's worst-case scenario nor the Phrynosoma-only model scenario from Case Studies I and II (Fig. 1).”
§ Rethinking phylogenetic comparative methods > CASE STUDY III: DARWIN'S SCENARIO AND UNREPLICATED BURSTS
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In the case of the PE hypothesis, we show that it does indeed have explanatory power beyond simply explaining a singular shift in Phrynosoma and support the original authors' conclusions.”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“If so, then any number of causal factors that differ between Phrynosoma and other lizards could be equally as likely as PE-including FM with a slight reclassification of character states!”
§ Rethinking phylogenetic comparative methods > CASE STUDY II: ADAPTIVE HYPOTHESES AND SINGULAR SHIFTS
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
A claim is checked only against the cited paper’s full text, never its abstract, and none is available for its sources.
In the paper
“While today we have a much wider range of comparative models to choose from including some that allow for adaptive shifts, most continuous trait models are Gaussian (e.g., Pagel 1999;Blomberg et al. 2003;Butler and King 2004;O'Meara et al. 2006;Eastman et al. 2011;Beaulieu et al. 2012;Uyeda and Harmon 2014) and do not accommodate abrupt, discontinuous shifts in phenotypes.”
§ Rethinking phylogenetic comparative methods > CASE STUDY I: FELSENSTEIN'S WORST-CASE SCENARIO
What the sources say
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In all three scenarios, something novel and interesting happened on a single branch and the distribution of traits at the tips of the phylogeny reflects this.”
§ Rethinking phylogenetic comparative methods > CASE STUDY III: DARWIN'S SCENARIO AND UNREPLICATED BURSTS
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The resolution of Simpson's paradox rests entirely on causal assumptions; which are immediately apparent from graphical models but difficult to express with standard mathematical formulae.”
- Also stated in: § CONCLUDING REMARKS: ARE OUR MODELS VALID · plain
“The resolution of Simpson's paradox rests entirely on causal assumptions; which are immediately apparent from graphical models but difficult to express with standard mathematical formulae.”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Also stated in: § CONCLUDING REMARKS: ARE OUR MODELS VALID · plain
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We also note that all the phylogenetic signal is coming from the evolution of body size, which becomes irrelevant once we observe body size, and thus we do not need to perform PGLS.”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- The authors state this as an assumption: Body size influences migratory behavior (in the illustrative example).
In the paper
“One way to gain a foothold on the problem of causation is to build, communicate, and analyze PCMs in a graphical modeling framework-a perspective that has recently been advocated by Höhna et al. (2014Höhna et al. ( , 2016)).”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
What the sources say
- Not matchedcites Höhna et al. (2014, 2016)
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence.
- Not matched
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In Case Study II, we present one solution to the problem that involves explicitly accounting for the possibility of unaccounted adaptive shifts using Bayesian Mixture modeling.”
§ Rethinking phylogenetic comparative methods > THE STRUCTURE OF A SOLUTION
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In our example, a four species phylogeny provides possible pathways for causal effects, but variables may have entirely nonphylogenetic causes or may be blocked from ancestral causes by observed measurements, rendering the phylogeny irrelevant (e.g., Fig. 7A).”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The remarkable coincidence is not just that the two characters happened to evolve on the same branch but that they were never subsequently gained or lost throughout the rest of the tree.”
§ Rethinking phylogenetic comparative methods > CASE STUDY III: DARWIN'S SCENARIO AND UNREPLICATED BURSTS
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We have shown that discontinuous processes and singular events are poorly handled in our current framework and lead to much confusion about what exactly, our statistical methods are allowing us to infer from comparative data.”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“As we illustrate through our Case Studies, we think that accounting for the possibility of idiosyncratic evolutionary events will be an essential step towards such a solution.”
§ Rethinking phylogenetic comparative methods > THE STRUCTURE OF A SOLUTION
plaindirectn = 3- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This is in large part because comparative data and the phylogeny that underly it are largely beyond the control of the researcher, but careful consideration of the data is required to understand what research questions can be reasonably answered.”
§ Rethinking phylogenetic comparative methods > CONCLUDING REMARKS: ARE OUR MODELS VALID
plain- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For example, it is common practice among systematists to search for defining and diagnostic characteristics for named clades; these traits are of especial interest and are likely the same sorts of traits that are researchers might include in comparative analysis, thereby greatly increasing the likelihood of finding traits with independent, unrelated origins that align with Darwin's scenario.”
§ Rethinking phylogenetic comparative methods > CASE STUDY III: DARWIN'S SCENARIO AND UNREPLICATED BURSTS
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“And it is clear from reading the macroevolutionary literature, biologists do not shy away from forming causal statements from correlative data regardless.”
§ Rethinking phylogenetic comparative methods > THE STRUCTURE OF A SOLUTION
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“but we do think that any compelling solution will involve a unification of phylogenetic natural history and hypothesis-testing approaches.”
§ Rethinking phylogenetic comparative methods > THE STRUCTURE OF A SOLUTION
plain- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper may give no reason why it holds.
In the paper
“We ultimately disagree with them that this constitutes a weak conclusion; the challenges of making these inferences from any comparative data set are significant.”
§ Rethinking phylogenetic comparative methods > THE STRUCTURE OF A SOLUTION
What the sources say
- Not checked — no full text of the sourcecites Maddison and FitzJohn (2015) source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, such intermediate cases will only introduce slight differences and may not be distinguishable from the fully dependent case under Darwin's Scenario (though they will be important in more intermediate cases, see Supplementary Material available on Dryad).”
§ Rethinking phylogenetic comparative methods > CASE STUDY III: DARWIN'S SCENARIO AND UNREPLICATED BURSTS
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Understanding the exact mathematical reasons why Pagel's test infers a significant correlation in a given case provides a clear boundary condition that can help develop quantitative corrections for ascertainment bias.”
§ Rethinking phylogenetic comparative methods > CASE STUDY III: DARWIN'S SCENARIO AND UNREPLICATED BURSTS
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Therefore, we are assured that increasing body size will likewise always decrease species abundance.”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- The authors state this as an assumption: Migratory behavior causes changes in body size (in the illustrative example).
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, under network (B) the correct method is PGLS (gray line) as increasing body size will have no effect on migratory behavior, and unaccounted phylogenetic residual error is present in the observed data.”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- The authors state this as an assumption: Migratory behavior causes changes in body size (in the illustrative example).
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“By explicitly including phylogeny into our graphical models of causation, we are forced to reckon with the scope of the inference problem and the ability of our data to be informative.”
§ Rethinking phylogenetic comparative methods > CONCLUDING REMARKS: ARE OUR MODELS VALID
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This is because increasing body size will simultaneously decrease species abundance and increase migratory behavior, which itself increases abundance, leading to a net slight increase in abundance.”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- The authors state this as an assumption: Body size influences migratory behavior (in the illustrative example).
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“By making our models explicit, we see that the phylogeny is best thought of as a pathway for past factors to causally influence the present-day distribution of observed states.”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“As a result, extending our analytical approach to more complicated scenarios will likely provide an even more meaningful estimate of the weight of evidence supporting a hypothesis of correlation.”
§ Rethinking phylogenetic comparative methods > CASE STUDY III: DARWIN'S SCENARIO AND UNREPLICATED BURSTS
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
In the paper
“Maddison and FitzJohn (2015) hinted that the coincident occurrence of single events could be a way of measuring the evidence for a correlation, but did not work out the details as we have done here.”
§ Rethinking phylogenetic comparative methods > CASE STUDY III: DARWIN'S SCENARIO AND UNREPLICATED BURSTS
What the sources say
- Not checked — no full text of the sourcecites Maddison and FitzJohn (2015) source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Indeed, we find that in all three Case Studies, the uniting philosophy is to consider models that account for background shifts in evolutionary regime, rather than strict adherence to a particular methodology.”
§ Rethinking phylogenetic comparative methods > THE STRUCTURE OF A SOLUTION
plainn = 3- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Furthermore, the issues of ascertainment bias are likely to rapidly dissipate as we move away from the boundary case of Darwin's scenario.”
§ Rethinking phylogenetic comparative methods > CASE STUDY III: DARWIN'S SCENARIO AND UNREPLICATED BURSTS
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, from our example of bird size and abundance, it is apparent that Westoby et al. were right all along: PCMs are a powerful tools for drawing inferences from interspecific data but they necessarily imply some types of causal structures and negate others.”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Westoby and colleagues were concerned that including phylogeny in interspecific comparisons necessarily favored some causal explanations over others.”
§ Rethinking phylogenetic comparative methods > PHYLOGENIES ARE GRAPHICAL MODELS OF CAUSATION
What the sources say
- Not matchedcites Westoby et al. (1995a,b)
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
- Not matched
The paper relies on this without support.
Descent with modification causes closely related species to be similar to one another in many traits.
“As a result of the process of descent with modification, closely related species tend to be similar to one another in a myriad different ways.”
The authors state this as an assumption.
Trait correlations can result from a single random shift drawn from a different distribution than the one used to model trait evolution across the rest of the branches.
“We can do so by including another phylogenetically plausible model: that trait correlations result from a single random shift, drawn from a different distribution than the one used to model trait evolution across the rest of the branches.”
The authors state this as an assumption.
The macroevolutionary optimum of a particular species is a weighted average of past regimes, as is typical in all OU models with discrete shifts in regimes.
“we consider the macroevolutionary optimum of a particular species to be a weighted average of past regimes, as is typical in all OU models with discrete shifts in regimes (Butler and King 2004;Beaulieu et al. 2012)”
The authors state this as an assumption.
The traits were selected for study without first looking at their phylogenetic distribution.
“we assume that the traits were selected for study without first looking at their phylogenetic distribution, a condition that we (as well as Maddison and FitzJohn 2015) suspect is rarely met in practice”
The authors state this as an assumption.
The likelihood of evolving these traits at all is quite small.
“we can make the assumption that the likelihood of evolving these traits at all is quite small”
The authors state this as an assumption.
Under Markovian assumptions, replaying the tape of life will likely lead to many worlds where milk and middle ear bones don't exist at all.
“In other words, replaying the tape of life, under Markovian assumptions, will likely lead to many worlds where milk and middle ear bones don't exist at all.”
The authors state this as an assumption.
The rates of gain of the traits are so low that only one shift is ever observed.
“Particularly, we assume that the rates of gain of the traits are so low that only one shift is ever observed.”
The authors state this as an assumption.
Ancestors are causes of descendants, and not vice versa.
“the nature of phylogenies allows us to assume that ancestors are causes of descendants, and not vice versa”
The authors state this as an assumption.
Body size influences migratory behavior (in the illustrative example).
“If we assume that body size influences migratory behavior”
The authors state this as an assumption.
Migratory behavior causes changes in body size (in the illustrative example).
“if migratory behavior causes changes in body size”
The authors state this as an assumption.
The rates of gain of the traits are so low that only one shift is ever observed (in the Figure 6 analysis).
“we assume that the rates of gain of the traits are so low that only one shift is ever observed”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Hence, in the extreme, very large datasets will almost always produce significant P-values, even if the estimated effect size is relatively small122 (Fig. 4).”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [122]
Experimental — accuracy not yet measured
Citations
Cites
Data Analysis Using Regression and Multilevel/Hierarchical Models
Gelman, A., & Hill, J. (2006) · doi:10.1017/cbo9780511790942 · Cited by 13,597
Causality: Models, Reasoning, and Inference
Pearl, J. (2009) · doi:10.1017/cbo9780511803161 · Cited by 11,653
Phylogenies and the Comparative Method
Felsenstein, J. (1985) · The American Naturalist · doi:10.1086/284325 · Cited by 9,793
Inferring the historical patterns of biological evolution
Pagel, M. (1999) · Nature · doi:10.1038/44766 · Cited by 5,200
TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE
Blomberg, S. P., Garland, T., & Ives, A. R. (2003) · Evolution · doi:10.1111/j.0014-3820.2003.tb00285.x · Cited by 4,678
Data Analysis Using Regression and Multilevel/Hierarchical Models
Gelman, A., & Su, Y.-S. (2007) · CRAN: Contributed Packages · doi:10.32614/cran.package.arm · Cited by 4,629
A likelihood approach to estimating phylogeny from discrete morphological character data
Lewis, P. O. (2001) · Systematic Biology · doi:10.1080/106351501753462876 · Cited by 2,929
A second course in stochastic processes
Karlin, S., & Taylor, H. E. (1981) · Cited by 2,770
Punctuated equilibria: the tempo and mode of evolution reconsidered
Gould, S. J., & Eldredge, N. (1977) · Paleobiology · doi:10.1017/s0094837300005224 · Cited by 2,628
Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence
Freckleton, R. P., Harvey, P. H., & Pagel, M. (2002) · The American Naturalist · doi:10.1086/343873 · Cited by 2,604
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The Phylogenetic Study of Adaptive Zones: Has Phytophagy Promoted Insect Diversification?
Mitter, C. W., Farrell, B. D., & Wiegmann, B. M. (1988) · The American Naturalist · doi:10.1086/284840 · Cited by 695
Huey, R. B., Garland, T., & Turelli, M. (2019) · The American Naturalist · doi:10.1086/703055 · Cited by 594
Fungal functional ecology: bringing a trait‐based approach to plant‐associated fungi
Zanne, A. E., Abarenkov, K., Afkhami, M. E., Aguilar‐Trigueros, C. A., Bates, S. T., Bhatnagar, J. M., Busby, P. E., Christian, N., Cornwell, W. K., Crowther, T. W., et al. (2019) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12570 · Cited by 285
The Role of Transposable Elements in Speciation
Serrato-Capuchina, A., & Matute, D. R. (2018) · Genes · doi:10.3390/genes9050254 · Cited by 210
Caetano, D. S., O’Meara, B. C., & Beaulieu, J. M. (2018) · Evolution · doi:10.1111/evo.13602 · Cited by 189
Metadata
- Authors
- Uyeda, J. C., Zenil-Ferguson, R., & Pennell, M. W.
- Affiliations
- Virginia Tech (US)
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844 USA
- University of British Columbia (CA)
- Corresponding author
- Uyeda, Josef C
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-04-25
- Volume
- 67
- Issue
- 6
- Pages
- 1091-1109
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2951967147
- Cited by
- 313
- References
- 113
- Citations by year
- 2026: 23 · 2025: 40 · 2024: 39 · 2023: 53 · 2022: 37 · 2021: 40 · 2020: 24 · 2019: 39 · 2018: 16
- FWCI
- 22.03
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Systematic Biology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- NSERC Discovery
- NSF (DEB-1208912, DBI-1661516)
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Morphological variations and asymmetry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- phylogenetic comparative analysis, hypothesis testing, causal inference, probabilistic graphical models, phylogeny, comparative biology
- MeSH terms
- Classification, Phylogeny
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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